We have developed anew protein identification software routine called "PepFrag", which is tuned to allow rapid, confident identification of proteins using our newly developed MALDI-ion trap mass spectrometer. This program, which was written by David Fenyo (a member of our Research Resource), is publicly available over the World Wide Web [http://chait-sgi.rockefeller.edu] and instantly accessible on all the computers within our laboratory. The identification strategy is based upon ideas proposed by others with a number of modifications and improvements tuned to the particular fragmentation properties of our MALDI-ITMS instrument. The program (1) searches the specified database for all peptides of the specified mass that can be generated by the specified enzyme from all proteins that are known from the specified species and (2) determines the subset of peptides that can give the specified ion fragments. A paper describing these developments has been submitted for publication..